Gene Expression Analysis of Blood PBMC Response to Mycobacterium leprae antigens
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE179987 | GEO | 2021/07/16
REPOSITORIES: GEO
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Project description:Leprosy is classified from paucibacillary leprosy (TT and BT) to multibacillary leprosy (BB, BL, and LL). In our study, we focus on selecting or classfying the significant genes to discriminate between paucibacillary and multibacillary group and the important genes to distinguish between blood and the corresponding tissue in patients.
2011-03-17 | GSE24280 | GEO
Project description:Leprosy is classified from paucibacillary leprosy (TT and BT) to multibacillary leprosy (BB, BL, and LL). In our study, we focus on selecting or classfying the significant genes to discriminate between paucibacillary and multibacillary group and the important genes to distinguish between blood and the corresponding tissue in patients. · Human Adult Normal Skin Sample (Commercial;Cat#1234218); 6 patients of leprosy (Blood and Tissue sample (Pathologic classification: BT); 6 patients of leprosy (Blood and Tissue sample (Pathologic classification: MB)) · In blood sample, BT sample vs MB sample · In tissue sample, Normal Skin sample vs tissue BT sample or tissue MB sample · Single Color Microarray · All experiments are performed one replicate
2011-03-17 | E-GEOD-24280 | biostudies-arrayexpress
Project description:Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation –– before and after stimulation with M. leprae sonicate in whole blood cells. We show that M. leprae antigen stimulation mainly triggered the upregulation of immune related genes and that a substantial proportion of the differential gene expression is genetically controlled. Indeed, using stringent criteria, we identified 318 genes displaying cis-eQTL at an FDR of 0.01, including 66 genes displaying response-eQTL (reQTL), i.e. cis-eQTL that showed significant evidence for interaction with the M. leprae stimulus. Such reQTL correspond to regulatory variations that affect the interaction between human whole blood cells and M. leprae sonicate, and thus likely between the human host and M. leprae bacilli. We found that reQTL are significantly enriched among binding sites of transcription factors that are activated in response to infection, and that they were enriched among single nucleotide polymorphisms (SNPs) associated with susceptibility to leprosy per se and Type-I Reaction, as well as SNPs targeted by recent positive selection. Our study suggests that natural selection shaped our genomic diversity to face pathogen exposure including M. leprae infection.
2017-07-07 | GSE100853 | GEO
Project description:Leprosy is major public health problem in developing countries. M. leprae infects human macrophages and Schwann cells leading to a chronic disease. Leprosy studies are constrained due to the lack of in vitro growth system for M. leprae. Moreover, the overall pathogenesis is poorly understood although the expression of some pro-inflammatory cytokines is associated with nerve damage that occurs during the infection. PBMC may participate of the host response to M. leprae infection leading to the inflammatory profile. We aimed to investigate the global human gene expression profile of human PBMC exposed to M. leprae for 4 H. Due to the reduced supply of M. leprae our study was restricted to three chips, including a dye-swap set. Our analysis revealed gene expression differences in cell receptors, NF-kB signaling and oxidative stress response. The results were confirmed by Real-time PCR and flow-cytometry and point to new insights into the molecular events resulted from host-pathogen interaction We analyzed 3 oligo-human chips, 10K elements each, spotted in duplicates. Two chips were replicas and one a dye-swap
2007-09-01 | E-GEOD-5765 | biostudies-arrayexpress
Project description:Leprosy is major public health problem in developing countries. M. leprae infects human macrophages and Schwann cells leading to a chronic disease. Leprosy studies are constrained due to the lack of in vitro growth system for M. leprae. Moreover, the overall pathogenesis is poorly understood although the expression of some pro-inflammatory cytokines is associated with nerve damage that occurs during the infection. PBMC may participate of the host response to M. leprae infection leading to the inflammatory profile. We aimed to investigate the global human gene expression profile of human PBMC exposed to M. leprae for 4 H. Due to the reduced supply of M. leprae our study was restricted to three chips, including a dye-swap set. Our analysis revealed gene expression differences in cell receptors, NF-kB signaling and oxidative stress response. The results were confirmed by Real-time PCR and flow-cytometry and point to new insights into the molecular events resulted from host-pathogen interaction Keywords: Modulation of human PBMC gene expression by M. leprae
2007-09-01 | GSE5765 | GEO
Project description:Mineralised dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. In this study we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of 16th century human dental calculus from an individual from Trondheim, Norway. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. M. leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual’s dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record.
2020-10-19 | PXD017836 | Pride
Project description:To this date, host transcriptome studies in leprosy have focused on Schwann cells, as well as mouse-footpad and skin biopsies. Despite macrophages being the most infected cell types in leprosy lesions, there is no genome-wide experiments with this model. Here, we aimed at identifying host macrophages transcriptional changes induced by live-Mycobacterium leprae infection for 48 hours.
2021-04-16 | GSE162416 | GEO
Project description:Mycobacterium leprae, the causative agent of leprosy, an obligate intracellular pathogen has the ability to survive and grow for extended periods within phagocytes and Schwann cells. M. leprae genome analysis predicts a highly degraded genome resulting in a significant loss of its genomic coding capacity. Detailed dynamics of carbon sources for energy utilization and growth of M. leprae is unclear. This study, therefore, presents M. leprae transcriptome during in vivo growth and ex vivo stationary phases, and explores metabolic pathways relevant to its growth from global gene expression data. This report provides a glimpse of some of M. leprae nutritional requirements for growth, which most likely, needs to be supplemented, in an axenic growth media.
2022-01-01 | GSE188532 | GEO
Project description:Mycobacterium leprae sequencing from recurrent leprosy cases
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Project description:Approximately half of M. lepraeâ??s transcriptome consists of inactive gene products. This has an impact on overall energy and resource consumption without potential benefit to this organism. However, multiple translational â??silencingâ?? mechanisms are present, reducing additional energy and resource expenditure required for protein production from these transcripts. The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and translational potentials should increase our understanding of their impact on M. leprae physiology. To address this, M. leprae was purified from the granulomatous hind footpad tissue of four individual nu/nu nude mice six months post-infection. M. leprae whole genome DNA microarrays representing the 1,614 annotated ORFs and 1,133 identified pseudogenes, were obtained from the Leprosy Research Support and Maintenance of an Armadillo Colony Post-Genome Era, Part I: Leprosy Research Support Contract (NO1 AI-25469) at Colorado State University. To validate 20% of genes positive by microarray analysis, RT-PCR was performed. Results of this study Gene expression analysis identified transcripts from 49% of all M. leprae genes including 57% of all ORFs and 43% of all pseudogenes in the genome. Pseudogenes were randomly distributed throughout the chromosome. Factors resulting in pseudogene transcription included: 1) co-orientation of transcribed pseudogenes with transcribed ORFs within or exclusive of operon-like structures; 2) the paucity of intrinsic stem-loop transcriptional terminators between transcribed ORFs and downstream pseudogenes; and 3) predicted pseudogene promoters. Mechanisms for translational silencing of pseudogene transcripts included the lack of both translational start codons and strong Shine-Dalgarno sequences. Transcribed pseudogenes also contained multiple in-frame stop codons and high Ka/Ks ratios, compared to that of homologs in M. tuberculosis and ORFs in M. leprae. A pseudogene transcript containing an active promoter, strong SD site, a start codon, but containing two in frame stop codons yielded a protein product when expressed in E. coli. Approximately half of M. leprae's transcriptome consists of inactive gene products consuming energy and resources without potential benefit to M. leprae. Presently it is unclear what additional detrimental affect(s) this large number of inactive mRNAs has on the functional capability of this organism. Translation of these pseudogenes may play an important role in overall energy consumption and resultant pathophysiological characteristics of M. leprae. However, this study also demonstrated that multiple translational silencing mechanisms are present, reducing additional energy and resource expenditure required for protein production from the vast majority of these transcripts. The overall design of this study was to identify the transcriptome of M. leprae in the granulomatous tissue of the mouse hind foot pad 6 months post infection.
2010-06-24 | E-GEOD-17191 | biostudies-arrayexpress